The Kiel In route can be selected when your at a little black dot at near the entrance. In order for the route to line up correctly you should be right on the dot and facing the entrance. This screen isn't from GWX so I can't show exact location. I put an x by the spot you need to be.
Getting attacked by the British in your home port in September 1939? I think that is unheard of. Are you sure you didn't sink some neutral ships in your first patrol. Sinking neutral ships, (one of the flotillas gives you practice targets but they are neutral) will make the German ships hostile to you. You may have been sunk by the German ships in Harbor.